| add_start_from(core::Real x, core::Real y, core::Real z) | protocols::ligand_docking::LigandDockProtocol | |
| append_ligand_docking_scores(core::pose::Pose const &before, core::pose::Pose const &after, core::scoring::ScoreFunctionCOP scorefxn, std::map< std::string, core::Real > &scores, protocols::toolbox::match_enzdes_util::EnzConstraintIOCOP constraint_io=nullptr) const | protocols::ligand_docking::LigandDockProtocol | |
| apply(core::pose::Pose &pose) override | protocols::ligand_docking::LigandDockProtocol | virtual |
| bb_interface_cutoff_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| choose_desired_centroid(core::pose::Pose const &pose, core::Size jump_id, utility::vector1< core::Vector >) | protocols::ligand_docking::LigandBaseProtocol | protected |
| classic_protocol(core::pose::Pose &pose, int jump_id, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo, core::Size num_cycles, core::Size repack_every_Nth) const | protocols::ligand_docking::LigandDockProtocol | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const | protocols::moves::Mover | virtual |
| create() | protocols::moves::Mover | virtual |
| Filters_map typedef | protocols::moves::Mover | |
| find_interface_backbone(core::pose::Pose const &pose, int jump_id, core::Real cutoff_dist, utility::vector1< bool > &is_interface, utility::vector1< bool > &is_around_interface) const | protocols::ligand_docking::LigandBaseProtocol | protected |
| find_interface_rsds(core::pose::Pose const &pose, int jump_id, core::Real padding, ObjexxFCL::FArray1D_bool &is_interface) const | protocols::ligand_docking::LigandBaseProtocol | protected |
| fresh_instance() const | protocols::moves::Mover | virtual |
| get_additional_output() | protocols::moves::Mover | virtual |
| get_current_job() const | protocols::moves::Mover | |
| get_current_tag() const | protocols::moves::Mover | inline |
| get_input_pose() const | protocols::moves::Mover | |
| get_last_move_status() const | protocols::moves::Mover | |
| get_ligand_id(core::pose::Pose const &pose) | protocols::ligand_docking::LigandBaseProtocol | static |
| get_ligand_id(core::pose::Pose const &pose, core::Size jump_id) | protocols::ligand_docking::LigandBaseProtocol | static |
| get_ligand_jump_id(core::pose::Pose const &pose) | protocols::ligand_docking::LigandBaseProtocol | static |
| get_name() const override | protocols::ligand_docking::LigandDockProtocol | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_non_bb_clashing_rotamers(core::pose::Pose const &pose, core::Size seqpos, core::scoring::ScoreFunctionCOP scofx, utility::vector1< core::conformation::ResidueCOP > &accepted_rotamers) const | protocols::ligand_docking::LigandBaseProtocol | |
| get_scorefxn() | protocols::ligand_docking::LigandBaseProtocol | |
| get_scorefxn() const | protocols::ligand_docking::LigandBaseProtocol | |
| get_self_ptr() const | protocols::moves::Mover | inline |
| get_self_ptr() | protocols::moves::Mover | inline |
| get_self_weak_ptr() const | protocols::moves::Mover | inline |
| get_self_weak_ptr() | protocols::moves::Mover | inline |
| get_type() const | protocols::moves::Mover | inline |
| hard_scorefxn_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| ligand_chi_stddev_deg_ | protocols::ligand_docking::LigandDockProtocol | private |
| ligand_protonation_ | protocols::ligand_docking::LigandDockProtocol | private |
| ligand_shear_moves_ | protocols::ligand_docking::LigandDockProtocol | private |
| ligand_tether_stddev_Ang_ | protocols::ligand_docking::LigandDockProtocol | private |
| ligand_torsion_restraints_ | protocols::ligand_docking::LigandDockProtocol | private |
| LigandBaseProtocol() | protocols::ligand_docking::LigandBaseProtocol | |
| LigandDockProtocol() | protocols::ligand_docking::LigandDockProtocol | |
| LigandDockProtocol(std::string const &protocol, bool const minimize_ligand, bool const minimize_backbone, bool const tether_ligand, bool const mutate_same_name3, core::Real const ligand_chi_stddev_deg, core::Real const protein_CA_stddev_Ang, core::Real const ligand_tether_stddev_Ang_=-1, core::Size const ligand_shear_moves=0) | protocols::ligand_docking::LigandDockProtocol | |
| LigandDockProtocol(LigandDockProtocol const &)=delete | protocols::ligand_docking::LigandDockProtocol | private |
| make_dockmcm_mover(core::pose::Pose const &pose, int jump_id, protocols::moves::MoverOP repack_mover, protocols::moves::MoverOP rigbod_mover, core::kinematics::MoveMapOP movemap, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo) const | protocols::ligand_docking::LigandDockProtocol | private |
| make_movemap(core::pose::Pose const &pose, core::Size jump_id, core::Real sc_padding, bool include_all_rsds, bool include_backbone, bool include_ligands, bool include_water) const | protocols::ligand_docking::LigandBaseProtocol | protected |
| make_packer_task(core::pose::Pose const &pose, ObjexxFCL::FArray1D_bool const &allow_repack, bool ligand_protonation) const | protocols::ligand_docking::LigandBaseProtocol | protected |
| make_packer_task(core::pose::Pose const &pose, int jump_id, core::Real sc_padding, bool include_all_rsds, bool ligand_protonation) const | protocols::ligand_docking::LigandBaseProtocol | protected |
| make_packer_task_ligand_only(core::pose::Pose const &pose, int jump_id, bool ligand_protonation) const | protocols::ligand_docking::LigandBaseProtocol | protected |
| make_tweaked_scorefxn(std::string const &weights_tag, bool estat_exclude_protein, bool estat_upweight, bool hbonds_downweight) | protocols::ligand_docking::LigandBaseProtocol | protected |
| minimize_all_rsds_ | protocols::ligand_docking::LigandDockProtocol | private |
| minimize_backbone_ | protocols::ligand_docking::LigandDockProtocol | private |
| minimize_ligand_ | protocols::ligand_docking::LigandDockProtocol | private |
| minimize_water_ | protocols::ligand_docking::LigandDockProtocol | private |
| move_ligand_to_desired_centroid(core::pose::Pose &pose, core::Size jump_id, utility::vector1< core::Vector > start_from_pts) | protocols::ligand_docking::LigandBaseProtocol | protected |
| move_ligand_to_desired_centroid(core::pose::Pose &pose, core::Size jump_id, core::Vector desired_centroid) | protocols::ligand_docking::LigandBaseProtocol | protected |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| mover_is_unpublished() const | protocols::moves::Mover | virtual |
| mover_provides_citation_info() const | protocols::moves::Mover | virtual |
| name() | protocols::moves::Mover | inlinestatic |
| optimize_orientation3(core::pose::Pose &pose, int jump_id, core::Size lig_id) | protocols::ligand_docking::LigandDockProtocol | private |
| parse_my_tag(TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose) | protocols::moves::Mover | virtual |
| Pose typedef | protocols::moves::Mover | |
| PoseCOP typedef | protocols::moves::Mover | |
| protein_CA_stddev_Ang_ | protocols::ligand_docking::LigandDockProtocol | private |
| protocol_ | protocols::ligand_docking::LigandDockProtocol | private |
| provide_authorship_info_for_unpublished() const | protocols::moves::Mover | virtual |
| provide_citation_info() const | protocols::moves::Mover | virtual |
| random_conformer(core::pose::Pose &pose) const | protocols::ligand_docking::LigandDockProtocol | private |
| register_options() | protocols::moves::Mover | inlinestatic |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| reorder_foldtree_around_mobile_regions(core::pose::Pose &pose, core::Size const &jump_id, utility::vector1< bool > const &mobile_bb, core::Size const &lig_id) const | protocols::ligand_docking::LigandBaseProtocol | |
| repack_all_rsds_ | protocols::ligand_docking::LigandDockProtocol | private |
| reset_status() | protocols::moves::Mover | |
| restrain_ligand_chis(core::pose::Pose &pose) | protocols::ligand_docking::LigandDockProtocol | private |
| restrain_ligand_nbr_atom(core::pose::Pose &pose, core::Size lig_id, core::Real stddev_Angstroms) const | protocols::ligand_docking::LigandBaseProtocol | protected |
| restrain_protein_Calphas(core::pose::Pose &pose, utility::vector1< bool > const &is_restrained, core::scoring::func::FuncOP restr_func) const | protocols::ligand_docking::LigandBaseProtocol | |
| rottrials_all_rsds_ | protocols::ligand_docking::LigandDockProtocol | private |
| sc_interface_padding_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| scorefxn_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| setup_bbmin_foldtree(core::pose::Pose &pose, core::Size const &jump_id, core::Real cutoff_dist, core::Real stddev_Angstroms) | protocols::ligand_docking::LigandBaseProtocol | protected |
| shared_from_this() | protocols::ligand_docking::LigandDockProtocol | inline |
| shear_min_protocol(core::pose::Pose &pose, int jump_id, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo, core::Size num_cycles) const | protocols::ligand_docking::LigandDockProtocol | private |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| soft_scorefxn_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| start_from_pts_ | protocols::ligand_docking::LigandDockProtocol | private |
| Strings typedef | protocols::moves::Mover | |
| TagCOP typedef | protocols::moves::Mover | |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| tether_ligand_ | protocols::ligand_docking::LigandDockProtocol | private |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| unboundrot_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| use_soft_rep_ | protocols::ligand_docking::LigandBaseProtocol | protected |
| ~LigandBaseProtocol() override | protocols::ligand_docking::LigandBaseProtocol | |
| ~LigandDockProtocol() override | protocols::ligand_docking::LigandDockProtocol | |
1.8.7